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Title :   CRYSTAL STRUCTURE OF PYRIDOXAL PHOSPHATE BIOSYNTHETIC PROTEIN PDXA PA0593

Authors :   Y. Liu, X. Xu, A. Dong, M. Kudritskam, A. Savchenko, E. F. Pai, A. Joachim A. Edwards, Midwest Center For Structural Genomics (Mcsg)

Date :   22 Feb 05 (Deposition) - 05 Apr 05 (Release) - 05 Oct 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.01

Chains :   Asym./Biol. Unit : A,B

Keywords :   Pa0593, Pyridoxine Biosynthesis, Oxidoreductase, Structural Genomics, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Liu, X. Xu, A. Dong, M. Kudritskam, A. Savchenko, E. F. Pai, A. Edward
Crystal Structure Of Pyridoxal Phosphate Biosynthetic Protein Pdxa Pa0593
To Be Published
PubMed: search

Molecule 1 - 4-HYDROXYTHREONINE-4-PHOSPHATE DEHYDROGENASE 1
	Chains	:	A, B
	EC Number	:	1.1.1.262
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	PDXA1
	Organism Scientific	:	PSEUDOMONAS AERUGINOSA
	Organism Taxid	:	287
	Synonym	:	4-PHOSPHOHYDROXY-L-THREONINE DEHYDROGENASE 1

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 24)

No.	Name	Count	Type	Full Name
1	EOH	10	Ligand/Ion	ETHANOL
2	MG	2	Ligand/Ion	MAGNESIUM ION
3	MSE	12	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:1265 , EOH A:3000 , HOH A:4033 , HOH A:4059 , HIS B:1210	BINDING SITE FOR RESIDUE MG A 5000
02	AC2	SOFTWARE	HIS A:1210 , HOH A:4139 , HIS B:1165 , HIS B:1265 , EOH B:3001 , HOH B:4073	BINDING SITE FOR RESIDUE MG A 5001
03	AC3	SOFTWARE	MSE A:1150 , HIS A:1165 , HIS A:1265 , LEU A:1269 , ASP A:1295 , HOH A:4033 , HOH A:4059 , MG A:5000	BINDING SITE FOR RESIDUE EOH A 3000
04	AC4	SOFTWARE	HOH A:4139 , MG A:5001 , MSE B:1150 , HIS B:1165 , HIS B:1265 , LEU B:1269 , ASP B:1295 , HOH B:4073	BINDING SITE FOR RESIDUE EOH B 3001
05	AC5	SOFTWARE	CYS A:1107 , PHE A:1112 , ASN A:1126 , HOH A:4029	BINDING SITE FOR RESIDUE EOH A 3002
06	AC6	SOFTWARE	HIS A:1210 , PRO A:1244 , ASP A:1246 , THR A:1247	BINDING SITE FOR RESIDUE EOH A 3003
07	AC7	SOFTWARE	THR B:1163 , THR B:1164 , LEU B:1166 , ARG B:1179	BINDING SITE FOR RESIDUE EOH B 3004
08	AC8	SOFTWARE	LYS A:1273 , ASP A:1295	BINDING SITE FOR RESIDUE EOH A 3005
09	AC9	SOFTWARE	GLU A:1064 , ARG A:1065 , ALA A:1140 , ASP A:1141 , HIS A:1144 , THR A:1145 , ALA A:1146	BINDING SITE FOR RESIDUE EOH A 3006
10	BC1	SOFTWARE	GLU A:1043 , PRO A:1082 , VAL A:1083	BINDING SITE FOR RESIDUE EOH A 3007
11	BC2	SOFTWARE	ARG B:1004 , TRP B:1062 , HIS B:1111	BINDING SITE FOR RESIDUE EOH B 3008
12	BC3	SOFTWARE	GLY B:1156 , LEU B:1157 , ARG B:1158 , LEU B:1254 , CYS B:1257 , ASP B:1258 , HOH B:4360	BINDING SITE FOR RESIDUE EOH B 3009

(no "SS Bond" information available for 1YXO)

Asymmetric/Biological Unit

No.	Residues
1	Gly A:1241	-	Pro A:1242
2	Gly B:1241	-	Pro B:1242

(no "SAP(SNP)/Variant" information available for 1YXO)

(no "PROSITE Motif" information available for 1YXO)

(no "Exon" information available for 1YXO)

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:328
 aligned with PDXA_PSEAE | Q9I5U4 from UniProtKB/Swiss-Prot  Length:328

    Alignment length:328
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320        
          PDXA_PSEAE      1 MSLRFALTPGEPAGIGPDLCLLLARSAQPHPLIAIASRTLLQERAGQLGLAIDLKDVSPAAWPERPAKAGQLYVWDTPLAAPVRPGQLDRANAAYVLETLTRAGQGCLDGHFAGMITAPVHKGVINEAGIPFSGHTEFLADLTHTAQVVMMLATRGLRVALATTHLPLREVADAISDERLTRVARILHADLRDKFGIAHPRILVCGLNPHAGEGGHLGREEIEVIEPCLERLRGEGLDLIGPLPADTLFTPKHLEHCDAVLAMYHDQGLPVLKYKGFGAAVNVTLGLPIIRTSVDHGTALDLAGSGRIDSGSLQVALETAYQMAASRC  328
               SCOP domains d1yxoa_ A: automated matches                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains -1yxoA00 A:1002-1328 Isopropylmalate Dehydrogenase                                                                                                                                                                                                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee......hhhhhhhhhh.......eeeeehhhhhhhhhhhhh...eeee..............eeeeee............hhhhhhhhhhhhhhhhhhhhh....eeee...hhhhhhhh.....hhhhhhhhhh.....eeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee..hhhhhh.....hhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhh...eeee.hhhhhhhhhhhhhh...eeeee.....eeee....hhhhh......hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1yxo A 1001 mSLRFALTPGEPAGIGPDLCLLLARSAQPHPLIAIASRTLLQERAGQLGLAIDLKDVSPAAWPERPAKAGQLYVWDTPLAAPVRPGQLDRANAAYVLETLTRAGQGCLDGHFAGmITAPVHKGVINEAGIPFSGHTEFLADLTHTAQVVmmLATRGLRVALATTHLPLREVADAISDERLTRVARILHADLRDKFGIAHPRILVCGLNPHAGEGGHLGREEIEVIEPCLERLRGEGLDLIGPLPADTLFTPKHLEHCDAVLAmYHDQGLPVLKYKGFGAAVNVTLGLPIIRTSVDHGTALDLAGSGRIDSGSLQVALETAYQmAASRC 1328
                            |     1010      1020      1030      1040      1050      1060      1070      1080      1090      1100      1110    | 1120      1130      1140      1150|     1160      1170      1180      1190      1200      1210      1220      1230      1240      1250      1260  |   1270      1280      1290      1300      1310      1320  |     
                            |                                                                                                              1115-MSE                           1150-MSE                                                                                                         1263-MSE                                                    1323-MSE 
                         1001-MSE                                                                                                                                              1151-MSE

Chain B from PDB  Type:PROTEIN  Length:328
 aligned with PDXA_PSEAE | Q9I5U4 from UniProtKB/Swiss-Prot  Length:328

    Alignment length:328
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320        
          PDXA_PSEAE      1 MSLRFALTPGEPAGIGPDLCLLLARSAQPHPLIAIASRTLLQERAGQLGLAIDLKDVSPAAWPERPAKAGQLYVWDTPLAAPVRPGQLDRANAAYVLETLTRAGQGCLDGHFAGMITAPVHKGVINEAGIPFSGHTEFLADLTHTAQVVMMLATRGLRVALATTHLPLREVADAISDERLTRVARILHADLRDKFGIAHPRILVCGLNPHAGEGGHLGREEIEVIEPCLERLRGEGLDLIGPLPADTLFTPKHLEHCDAVLAMYHDQGLPVLKYKGFGAAVNVTLGLPIIRTSVDHGTALDLAGSGRIDSGSLQVALETAYQMAASRC  328
               SCOP domains d1yxob_ B: automated matches                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains -1yxoB00 B:1002-1328 Isopropylmalate Dehydrogenase                                                                                                                                                                                                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee......hhhhhhhhhhhh.....eeeeehhhhhhhhhhhhh...eeee..............eeeeee............hhhhhhhhhhhhhhhhhhhhh....eeee...hhhhhhhh.....hhhhhhhhhh.....eeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee..hhhhhh.....hhhhhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhh...eeee.hhhhhhhhhhhhh....eeeee.....eeee....hhhhh......hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1yxo B 1001 mSLRFALTPGEPAGIGPDLCLLLARSAQPHPLIAIASRTLLQERAGQLGLAIDLKDVSPAAWPERPAKAGQLYVWDTPLAAPVRPGQLDRANAAYVLETLTRAGQGCLDGHFAGmITAPVHKGVINEAGIPFSGHTEFLADLTHTAQVVmmLATRGLRVALATTHLPLREVADAISDERLTRVARILHADLRDKFGIAHPRILVCGLNPHAGEGGHLGREEIEVIEPCLERLRGEGLDLIGPLPADTLFTPKHLEHCDAVLAmYHDQGLPVLKYKGFGAAVNVTLGLPIIRTSVDHGTALDLAGSGRIDSGSLQVALETAYQmAASRC 1328
                            |     1010      1020      1030      1040      1050      1060      1070      1080      1090      1100      1110    | 1120      1130      1140      1150|     1160      1170      1180      1190      1200      1210      1220      1230      1240      1250      1260  |   1270      1280      1290      1300      1310      1320  |     
                            |                                                                                                              1115-MSE                           1150-MSE                                                                                                         1263-MSE                                                    1323-MSE 
                         1001-MSE                                                                                                                                              1151-MSE

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric/Biological Unit

Classes(

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Folds(

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Superfamilies( (-)

)

Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: Alpha and beta proteins (a/b) (23833)

Fold: Isocitrate/Isopropylmalate dehydrogenase-like (143)

Superfamily: Isocitrate/Isopropylmalate dehydrogenase-like (143)

Family: PdxA-like (6)

Protein domain: automated matches (2)

Pseudomonas aeruginosa [TaxId: 287] (1)

1a	d1yxoa_	A:
1b	d1yxob_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Isopropylmalate Dehydrogenase (91)

Homologous Superfamily: Isopropylmalate Dehydrogenase (91)

Pseudomonas aeruginosa. Organism_taxid: 287. (1)

1a	1yxoA00	A:1002-1328
1b	1yxoB00	B:1002-1328

(no "Pfam Domain" information available for 1YXO)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (PDXA_PSEAE | Q9I5U4)

molecular function
	GO:0050570	4-hydroxythreonine-4-phosphate dehydrogenase activity	Catalysis of the reaction: 4-(phosphonooxy)-threonine + NAD+ = 2-amino-3-oxo-4-phosphonooxybutyrate + NADH + H+.
	GO:0051287	NAD binding	Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
	GO:0050897	cobalt ion binding	Interacting selectively and non-covalently with a cobalt (Co) ion.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0016616	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor	Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0042823	pyridoxal phosphate biosynthetic process	The chemical reactions and pathways resulting in the formation of pyridoxal phosphate, pyridoxal phosphorylated at the hydroxymethyl group of C-5, the active form of vitamin B6.
	GO:0008615	pyridoxine biosynthetic process	The chemical reactions and pathways resulting in the formation of pyridoxine, 2-methyl-3-hydroxy-4,5-bis(hydroxymethyl)pyridine, one of the vitamin B6 compounds.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric/Biological Unit
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		Gly B:1241 - Pro B:1242	[ RasMol ]

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Description

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Ligands, Modified Residues, Ions (3, 24)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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